From: Kevin C Chan (cchan2242-c_at_my.cityu.edu.hk)
Date: Mon Jun 15 2015 - 07:29:36 CDT
Thanks for the reply.
I have tried but I don't think charmm-GUI would give the file, either nor
the tgz downloaded directly from CHARMM.
Thanks in advance,
Kevin
On Mon, Jun 15, 2015 at 5:37 PM, Branko <bdrakuli_at_chem.bg.ac.rs> wrote:
> Kevin,
>
> Try to make parameters with charmm-GUI:
> http://www.charmm-gui.org/?doc=input
> Chose some small protein and solvate such system. Among parameters
> generated you can find this str file.
> Alternatively, check could this file can be found in
> 'toppar_c36_aug14.tgz' on http://mackerell.umaryland.edu/charmm_ff.shtml
>
> Branko
>
>
> On 6/15/2015 10:07 AM, Kevin C Chan wrote:
>
> Thanks Branko. It works perfectly fine until I met the stream files,
> e.g. toppar_water_ions.str. I looked back the thread and found you have
> already given hints on it. So how did you get that
> toppar_water_ions_namd.str? By deleting those CHARMM languages one by one?
>
> Thanks,
> Kevin
>
> On Fri, Jun 5, 2015 at 6:17 PM, Branko <bdrakuli_at_chem.bg.ac.rs> wrote:
>
>> Kevin,
>>
>> You not need to have single parameter file for NAMD simulation, just
>> specify parameters in namd configuration file, for example:
>>
>> parameters par_all36_carb.prm
>> parameters par_all36_cgenff.prm
>> parameters par_all36_lipid.prm
>> parameters par_all36_na.prm
>> parameters par_all36_prot.prm
>> parameters toppar_water_ions_namd.str - pay attention on this
>> line. CHARMM36 water and ions parameters for NAMD
>>
>> Alternatively you can use inp merge, built-in in VegaZZ (
>> http://nova.disfarm.unimi.it/cms/index.php?Software_projects:VEGA_ZZ)
>>
>> Branko
>>
>>
>> On 6/5/2015 11:51 AM, Kevin C Chan wrote:
>>
>> Dear Users,
>>
>> I guess there will be a quick answer. I am wondering how people usually
>> combine parameter files directly downloaded from CHARMM website to have the
>> par_all36_XXX.inp? For instance, we want to combine all the parameter files
>> from CHARMM36 to become one single inp to be read for my NAMD simulation.
>>
>> Thanks in advance,
>> Kevin
>> City University of Hong Kong
>>
>>
>>
>
>
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